AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species

BMC Plant Biology
Andrew J RobinsonMathew G Lewsey

Abstract

The genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Transcriptome data obtained by RNA-sequencing (RNA-Seq) is often deposited in public databases that are made available via data portals. Data visualization is one of the first steps in assessment and hypothesis generation. However, these databases do not typically include visualization tools and establishing one is not trivial for users who are not computational experts. This, as well as the various formats in which data is commonly deposited, makes the processes of data access, sharing and utility more difficult. Our goal was to provide a simple and user-friendly repository that meets these needs for data-sets from major agricultural crops. AgriSeqDB ( https://expression.latrobe.edu.au/agriseqdb ) is a database for viewing, analysing and interpreting developmental and tissue/cell-specific transcriptome data from several species, including major agricultural crops such as wheat, rice, maize, barley and tomato. The disparate manner in which public transcriptome data is often warehoused and the challenge of visualizing raw data are both major hurdles to data reuse. The popul...Continue Reading

References

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Citations

Oct 20, 2019·The Plant Journal : for Cell and Molecular Biology·Lim Chee LiewMathew G Lewsey
Sep 4, 2020·Nature·Prashanth Srinivasan, Christina D Smolke
Aug 31, 2019·Plants·Anna V Klepikova, Aleksey A Penin

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Methods Mentioned

BETA
RNA-Seq
MDS

Software Mentioned

eFP ) browser
GeneView ( eFP )
GeneView (
GEO
AgriSeqDB
Degust ) browser
GeneView
eFP browser
browser
Kallisto

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